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ezSegmentation #958

Merged
merged 123 commits into from
Nov 29, 2023
Merged

ezSegmentation #958

merged 123 commits into from
Nov 29, 2023

Commits on Mar 23, 2023

  1. added started ez_seg file + test

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  2. Merge branch 'main' into ezSegmenter/start

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  3. applied filters.threshold_local's output to create a binary mask

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  4. Merge branch 'main' into ezSegmenter/start

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Commits on Mar 24, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on Apr 13, 2023

  1. Adding merge_mask functionality to be later built into merge_masks no… 

    …tebook.
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Commits on Apr 17, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on Apr 19, 2023

  1. added composite builder functionality - ready for refactoring

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  2. merging updated branch locally

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Commits on May 15, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on May 17, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on May 22, 2023

  1. ezseg_v1 notebook

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  2. Merge branch 'main' into ezSegmenter/start

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Commits on Jun 27, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on Jul 5, 2023

  1. Second version of ez notebook started, changes to composite builder a… 

    …nd mask merging, as well as new within-notebook display functionality found in ez_seg_display.py.
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Commits on Jul 6, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on Jul 13, 2023

  1. Added a relabeleing step necessary for masks merging. Need to test it… 

    …'s mask vs channel import setup.
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  2. merging remote with local

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Commits on Jul 19, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on Jul 20, 2023

  1. refactor stage 1 

    refactor stage 2
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  2. Merge branch 'main' into ezSegmenter/start

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Commits on Jul 21, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on Jul 22, 2023

  1. refactoring pt.2 

    refactor

refactor pt.3
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Commits on Jul 25, 2023

  1. refactor pt. 3

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  2. Merge branch 'main' into ezSegmenter/start

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  3. added ez_seg folder in tests

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Commits on Aug 1, 2023

  1. switch order of composite builder & mask creator, added mask_name to … 

    …mask creator section of notebook
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Commits on Aug 10, 2023

  1. notebook adjustments

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  2. notebook adjustments v3

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  3. Merge branch 'main' into ezSegmenter/start

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  4. modified: templates/ez_testing/ezseg_v2.ipynb

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  5. Merge branch 'main' into ezSegmenter/start

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Commits on Aug 11, 2023

  1. refactor sections 1-3

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  2. removed unused import

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  3. renumber mask adjustments

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Commits on Sep 19, 2023

  1. Switched ordering of mask merge and mask relabeling. Additionally upd… 

    …ated cell table function with appropriate path names. Need to ensure this will loop through entire ez_masks to create a single table.
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  2. Renamed the dir input to cell table creation as root_mask_dir to acco… 

    …unt for additional sources of masks.
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Commits on Sep 22, 2023

  1. Composite builder now iterates over all input fov's. Bug fixed where … 

    …add & subtract weren't working due to array type of uint8 (changed to int).
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Commits on Sep 26, 2023

  1. Fixed problem with ez segmentation mask maker not performing size exc… 

    …lusion properly due to lack of boolean screen. Additionally re-wrote mask saving.
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Commits on Sep 29, 2023

  1. Updated visuals for composite, mask overlay. Updated notebook with mu… 

    …ltiple different input parameters for seg. Fixed issue with segmentation process where import of a folder with one tiff could not be read into _create_object_masks.
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Commits on Oct 4, 2023

  1. Updated display code and notebook cells for ez segmentation step.

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Commits on Oct 6, 2023

  1. Merge branch 'main' into ezSegmenter/start

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Commits on Oct 12, 2023

  1. Updated ez segmentation, merging, and mask display functions.

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  2. Merge branch 'ezSegmenter/start' of https://github.com/angelolab/ark-… 

    …analysis into ezSegmenter/start
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  3. Fixed relabeline of all masks in merged mask dir.

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Commits on Oct 13, 2023

  1. base mantis project for ezseg data

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  2. docs, nb cleanup

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  3. ezseg_utils fix

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Commits on Oct 17, 2023

  1. Updated ez object cell table creation in marker_quantification file. … 

    …Additional package loading fixes done.
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  2. merging changes between mantis and marker_quant updates.

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Commits on Oct 18, 2023

  1. Refactored ez notebook and modules, added log creator.

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  2. cleaned up naming, variable, errors across all ez code.

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Commits on Oct 19, 2023

  1. Final code quality changes for v1 publish.

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Commits on Oct 24, 2023

  1. Changes for merge.

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  2. Code and ouput cleanup.

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Commits on Oct 25, 2023

  1. Merge branch 'main' into ezSegmenter/start

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  2. More cleanup before merge.

    @bryjcannon
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  3. Merging from main.

    @bryjcannon
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  4. Removed old templates.

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  5. notebook cleanup

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Commits on Oct 27, 2023

  1. Initial commit of ezSegmenter example dataset integration

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  2. Initial notebook commit

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Commits on Oct 30, 2023

  1. Merge remote-tracking branch 'origin/ezSegmenter/start' into ezSegmen… 

    …ter/start
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  2. Fix CI file to use Python 3.11

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  3. Skip the create_object_masks test

    @alex-l-kong
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  4. Remove syntax errors

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  5. Doc fixes

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  6. Type hinting fix

    @alex-l-kong
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  7. Add full notebook testing for ez_segmenter notebook

    @alex-l-kong
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  8. More doc fixes (multiple_mask_displays)

    @alex-l-kong
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  9. Update tests for ezSeg example dataset

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Commits on Oct 31, 2023

  1. Officially merge ezSegmenter example dataset in

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  2. Merge branch 'main' into ezSegmenter/start

    @alex-l-kong
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  3. Ensure easier naming of files by specifying additional path to ezSegm… 

    …entation directory
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Commits on Nov 1, 2023

  1. Changed example data dir structure.

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Commits on Nov 6, 2023

  1. Clean up path specification for example dataset ez_seg data download

    @alex-l-kong
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  2. Account for new 'mask_type' column that gets generated in the cell table

    @alex-l-kong
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  3. Fix marker_quantification tests

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Commits on Nov 8, 2023

  1. Begin adding tests for ez_seg_utils.py

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Commits on Nov 9, 2023

  1. Add all tests except for split_csvs_by_mask

    @alex-l-kong
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  2. Added image directory subfolder capability to composites, ez_obj_seg,… 

    … plus other minor fixes.
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  3. CSV filter testing fleshed out

    @alex-l-kong
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  4. Make sure csv_substr_replace arg gets updated in notebook too

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  5. Merge remote-tracking branch 'origin/ezSegmenter/start' into ezSegmen… 

    …ter/start
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  6. Doc fixes

    @alex-l-kong
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  7. Updated display functions with subfolder access.

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  8. Merge branch 'ezSegmenter/start' of https://github.com/angelolab/ark-… 

    …analysis into ezSegmenter/start
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  9. tests mostly finalized

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  10. Remove old start_jupyter.sh notebook

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  11. merge latest

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  12. Merge branch 'ezSegmenter/start' of github.com:angelolab/ark-analysis… 

    … into ezSegmenter/start
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  13. notebook tests, try CI

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  14. reran ez_seg nb

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Commits on Nov 10, 2023

  1. replace A | B with Union[A,B]

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  2. missed an Optional

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  3. as_posix -> as_uri, TestClusterMaskData fix

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  4. removed a platform specific assert

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  5. removed assert for fov_mapping

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Commits on Nov 13, 2023

  1. Fixed thresholding issue in seg, fixed csv sepeartion in utils.

    @bryjcannon
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  2. Merging remote and local

    @bryjcannon
    bryjcannon committed Nov 13, 2023
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  3. Ensure that if the csv file doesn't contain csv_to_replace, fix it

    @alex-l-kong
    alex-l-kong committed Nov 13, 2023
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  4. Merge remote-tracking branch 'origin/ezSegmenter/start' into ezSegmen… 

    …ter/start
    @alex-l-kong
    alex-l-kong committed Nov 13, 2023
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  5. Fix nbviewer notebook error.

    @bryjcannon
    bryjcannon committed Nov 13, 2023
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  6. Added readme information, fixed jupyter json error.

    @bryjcannon
    bryjcannon committed Nov 13, 2023
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Commits on Nov 17, 2023

  1. -1 -> 'auto' for clarity, rounded and set dtype to int after gaussian… 

    … filter in `ez_object_segmentation._create_object_mask`
    @srivarra
    srivarra committed Nov 17, 2023
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Commits on Nov 20, 2023

  1. Fixed subdirectory issue when using a composite image.

    @bryjcannon
    bryjcannon committed Nov 20, 2023
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  2. Add testing for merge masks

    @alex-l-kong
    alex-l-kong committed Nov 20, 2023
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  3. Merge remote-tracking branch 'origin/ezSegmenter/start' into ezSegmen… 

    …ter/start
    @alex-l-kong
    alex-l-kong committed Nov 20, 2023
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Commits on Nov 21, 2023

  1. Add full testing for composites.py

    @alex-l-kong
    alex-l-kong committed Nov 21, 2023
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  2. Remove print statements from composites.py

    @alex-l-kong
    alex-l-kong committed Nov 21, 2023
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  3. Ensure fixtures get reset for each test

    @alex-l-kong
    alex-l-kong committed Nov 21, 2023
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Commits on Nov 27, 2023

  1. Fixed segmentation issue due to a round error, updated displays, adde… 

    …d final_mask_dir util, notebook fixes.
    @bryjcannon
    bryjcannon committed Nov 27, 2023
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  2. Add testing for find_and_copy_files

    @alex-l-kong
    alex-l-kong committed Nov 27, 2023
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  3. Add missing notebook tags back and reformat notebook tests to preserv… 

    …e order
    @alex-l-kong
    alex-l-kong committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. Fixed a recursive file copy issue.

    @bryjcannon
    bryjcannon committed Nov 28, 2023
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  2. Merge branch 'ezSegmenter/start' of https://github.com/angelolab/ark-… 

    …analysis into ezSegmenter/start
    @alex-l-kong
    alex-l-kong committed Nov 28, 2023
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  3. Fix check for file to root

    @alex-l-kong
    alex-l-kong committed Nov 28, 2023
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  4. Coerce Path types to str for find_and_copy_files

    @alex-l-kong
    alex-l-kong committed Nov 28, 2023
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  5. Add new composite types to example_dataset_test

    @alex-l-kong
    alex-l-kong committed Nov 28, 2023
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  6. Update type annotation of find_and_copy_files to pathlib.Path, not Li… 

    …st[str]
    @alex-l-kong
    alex-l-kong committed Nov 28, 2023
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  7. Remove extraneous composite names

    @alex-l-kong
    alex-l-kong committed Nov 28, 2023
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  8. Update file names in new ezSegmenter example dataset

    @alex-l-kong
    alex-l-kong committed Nov 28, 2023
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Commits on Nov 29, 2023

  1. Formatting fix

    @alex-l-kong
    alex-l-kong committed Nov 29, 2023
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